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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/controller Controller2DModel.java,1.4,1.5 Controller2D.java,1.12,1.13
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From: Egon W. <eg...@us...> - 2003-12-22 09:20:40
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/controller
In directory sc8-pr-cvs1:/tmp/cvs-serv453/src/org/openscience/cdk/controller
Modified Files:
Controller2DModel.java Controller2D.java
Log Message:
Added trigger to auto update of # implicit hydrogens (implements JCP RFE #813152), and fixed lasso selection
Index: Controller2DModel.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/controller/Controller2DModel.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- Controller2DModel.java 21 Nov 2003 13:59:06 -0000 1.4
+++ Controller2DModel.java 22 Dec 2003 09:20:33 -0000 1.5
@@ -65,7 +65,9 @@
private double bondPointerLength = 20;
private double ringPointerLength = 20;
-
+
+ private boolean autoUpdateImplicitHydrogens = true;
+
/**
* Returns the draw mode.
*
@@ -140,11 +142,27 @@
return this.snapToGridAngle;
}
+ /**
+ * Returns true if the number of implicit hydrogens is updated
+ * when an Atom is edited.
+ */
+ public boolean getAutoUpdateImplicitHydrogens() {
+ return this.autoUpdateImplicitHydrogens;
+ }
+
+ /**
+ * Sets wether the number of implicit hydrogens is update when an
+ * Atom is edited.
+ */
+ public void setAutoUpdateImplicitHydrogens(boolean update) {
+ this.autoUpdateImplicitHydrogens = update;
+ }
+
/**
* Sets the snapToGridAngle mode
*
- * @param snapToGridAngle
+ * @param snapToGridAngle
*/
public void setSnapToGridAngle(boolean snapToGridAngle)
{
Index: Controller2D.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/controller/Controller2D.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- Controller2D.java 21 Dec 2003 19:22:37 -0000 1.12
+++ Controller2D.java 22 Dec 2003 09:20:33 -0000 1.13
@@ -37,6 +37,7 @@
import org.openscience.cdk.tools.ChemModelManipulator;
import org.openscience.cdk.tools.ReactionManipulator;
import org.openscience.cdk.tools.IsotopeFactory;
+import org.openscience.cdk.tools.HydrogenAdder;
import java.awt.*;
import java.util.*;
import java.awt.event.*;
@@ -57,7 +58,7 @@
Controller2DModel c2dm;
boolean wasDragged = false;
boolean isUndoableChange = false;
-
+
private Vector listeners = new Vector();
private LoggingTool logger;
@@ -70,6 +71,9 @@
private static Hashtable popupMenus = null;
+ // Helper classes
+ HydrogenAdder hydrogenAdder = new HydrogenAdder();
+
/**
* Constructs a controller that performs operations on the
* AtomContainer when actions are detected from the MouseEvents.
@@ -110,7 +114,7 @@
{
this.isUndoableChange = isUndoable;
}
-
+
public void setController2DModel(Controller2DModel model) {
this.c2dm = model;
}
@@ -196,7 +200,7 @@
*************************************************************************/
if (c2dm.getDrawMode() == c2dm.LASSO) {
/* Draw polygon in screencoordinates, convert them
- to world coordinates when mouse release */
+ to world coordinates when mouse released */
r2dm.addLassoPoint(new Point(event.getX(), event.getY()));
}
@@ -236,11 +240,11 @@
int mouseX = mouseCoords[0];
int mouseY = mouseCoords[1];
- logger.debug("MousePressed Event Props: mode=" + c2dm.getDrawModeString() +
+ logger.debug("MousePressed Event Props: mode=" + c2dm.getDrawModeString() +
", trigger=" + event.isPopupTrigger() +
", Button number: " + event.getButton() +
", Click count: " + event.getClickCount());
-
+
if (event.isPopupTrigger() || event.getButton() == MouseEvent.BUTTON3) {
logger.info("Popup menu triggered...");
popupMenuForNearestChemObject(mouseX, mouseY, event);
@@ -257,13 +261,13 @@
} else {
r2dm.setPointerVectorStart(new Point(mouseX, mouseY));
}
-
+
if (c2dm.getDrawMode() == c2dm.MOVE) {
selectNearestChemObjectIfNoneSelected(mouseX, mouseY);
}
}
}
-
+
/**
* manages all actions that will be invoked when a mouse button is released
@@ -271,12 +275,12 @@
* @param event MouseEvent object
**/
public void mouseReleased(MouseEvent event) {
-
- logger.debug("MouseReleased Event Props: mode=" + c2dm.getDrawModeString() +
+
+ logger.debug("MouseReleased Event Props: mode=" + c2dm.getDrawModeString() +
", trigger=" + event.isPopupTrigger() +
", Button number: " + event.getButton() +
", Click count: " + event.getClickCount());
-
+
if (event.getButton() == MouseEvent.BUTTON1) {
int[] screenCoords = { event.getX(), event.getY() };
int[] mouseCoords = getWorldCoordinates(screenCoords);
@@ -306,11 +310,22 @@
logger.error("Error while configuring atom");
logger.debug(exception);
}
+ // update atom
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ AtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atomInRange);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+
// also adjust the new draw elem
c2dm.setDrawElement(symbol);
-
- /* PRESERVE THIS. This notifies the
- * the listener responsible for
+
+ /* PRESERVE THIS. This notifies the
+ * the listener responsible for
* undo and redo storage that it
* should store this change of an atom symbol
*/
@@ -328,23 +343,46 @@
Atom atomInRange = r2dm.getHighlightedAtom();
if (atomInRange != null) {
atomInRange.setFormalCharge(atomInRange.getFormalCharge() + 1);
- /* PRESERVE THIS. This notifies the
- * the listener responsible for
+
+ // update atom
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ AtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atomInRange);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+
+ /* PRESERVE THIS. This notifies the
+ * the listener responsible for
* undo and redo storage that it
* should store this change of an atom charge
*/
isUndoableChange = true;
/* --- */
r2dm.fireChange();
- fireChange();
+ fireChange();
}
}
if (c2dm.getDrawMode() == c2dm.DECCHARGE) {
Atom atomInRange = r2dm.getHighlightedAtom();
if (atomInRange != null) {
atomInRange.setFormalCharge(atomInRange.getFormalCharge() - 1);
- /* PRESERVE THIS. This notifies the
- * the listener responsible for
+ // update atom
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ AtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atomInRange);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+
+ /* PRESERVE THIS. This notifies the
+ * the listener responsible for
* undo and redo storage that it
* should store this change of an atom symbol
*/
@@ -354,7 +392,7 @@
fireChange();
}
}
-
+
/*************************************************************************
* DRAWBONDMODE *
*************************************************************************/
@@ -366,7 +404,7 @@
int startY = r2dm.getPointerVectorStart().y;
Bond bondInRange = r2dm.getHighlightedBond();
atomInRange = r2dm.getHighlightedAtom();
-
+
if (bondInRange != null) {
// increase Bond order
double order = bondInRange.getOrder();
@@ -374,9 +412,22 @@
bondInRange.setOrder(CDKConstants.BONDORDER_SINGLE);
} else {
bondInRange.setOrder(order + 1.0);
- // this is tricky as it depends on the fact that the
+ // this is tricky as it depends on the fact that the
// constants are unidistant, i.e. {1.0, 2.0, 3.0}.
};
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ Atom[] atoms = bondInRange.getAtoms();
+ AtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atoms[0]);
+ for (int i=0; i<atoms.length; i++) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atoms[i]);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+ }
/* PRESERVE THIS. This notifies the
* the listener responsible for
* undo and redo storage that it
@@ -392,6 +443,16 @@
newAtom1 = new Atom(c2dm.getDrawElement(), new Point2d(startX,startY));
AtomContainer atomCon = ChemModelManipulator.createNewMolecule(chemModel);
atomCon.addAtom(newAtom1);
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(atomCon, newAtom1);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+
+ }
/* PRESERVE THIS. This notifies the
* the listener responsible for
* undo and redo storage that it
@@ -416,6 +477,18 @@
}
newBond = new Bond(newAtom1, newAtom2, 1);
atomCon.addBond(newBond);
+
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(atomCon, newAtom2);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+
+ }
+
/* PRESERVE THIS. This notifies the
* the listener responsible for
* undo and redo storage that it
@@ -448,6 +521,16 @@
atomCon.addAtom(newAtom2);
atomCon.addBond(new Bond(atomInRange, newAtom2, 1.0));
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(atomCon, atomInRange);
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(atomCon, newAtom2);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
}
}
r2dm.fireChange();
@@ -471,7 +554,7 @@
} else {
bondInRange.setStereo(CDKConstants.STEREO_BOND_UP);
};
- /* PRESERVE THIS. This notifies the
+ /* PRESERVE THIS. This notifies the
* the listener responsible for
* undo and redo storage that it
* should store this change of an atom symbol
@@ -521,6 +604,7 @@
*************************************************************************/
if (c2dm.getDrawMode() == c2dm.SELECT && wasDragged)
{
+ logger.info("User asks to selected atoms");
AtomContainer selectedPart = new AtomContainer();
r2dm.setSelectedPart(selectedPart);
r2dm.setSelectedPart(getContainedAtoms(r2dm.getSelectRect()));
@@ -536,13 +620,41 @@
Atom highlightedAtom = r2dm.getHighlightedAtom();
Bond highlightedBond = r2dm.getHighlightedBond();
if (highlightedAtom != null) {
+ logger.info("User asks to delete an Atom");
AtomContainer container = ChemModelManipulator.getAllInOneContainer(chemModel);
logger.debug("Atoms before delete: " + container.getAtomCount());
ChemModelManipulator.removeAtomAndConnectedElectronContainers(chemModel, highlightedAtom);
container = ChemModelManipulator.getAllInOneContainer(chemModel);
logger.debug("Atoms before delete: " + container.getAtomCount());
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ Atom[] atoms = container.getConnectedAtoms(highlightedAtom);
+ AtomContainer atomCon = ChemModelManipulator.getRelevantAtomContainer(chemModel, atoms[0]);
+ for (int i=0; i<atoms.length; i++) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(atomCon, atoms[i]);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+ }
} else if (highlightedBond != null) {
+ logger.info("User asks to delete a Bond");
ChemModelManipulator.removeElectronContainer(chemModel, highlightedBond);
+ // update atoms
+ if (c2dm.getAutoUpdateImplicitHydrogens()) {
+ Atom[] atoms = highlightedBond.getAtoms();
+ AtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atoms[0]);
+ for (int i=0; i<atoms.length; i++) {
+ try {
+ hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atoms[i]);
+ } catch (Exception exception) {
+ logger.error(exception.getMessage());
+ logger.debug(exception);
+ }
+ }
+ }
} else {
logger.warn("Cannot deleted if nothing is highlighted");
return;
@@ -577,7 +689,7 @@
int ringSize = c2dm.getRingSize();
String symbol = c2dm.getDrawElement();
AtomContainer sharedAtoms = getHighlighted();
-
+
/******************** NO ATTACHMENT ************************************/
if (sharedAtoms.getAtomCount() == 0) {
sharedAtoms = new AtomContainer();
@@ -657,7 +769,7 @@
isUndoableChange = true;
/* --- */
}
-
+
/*********************** FUSED *****************************************/
else if (sharedAtoms.getAtomCount() == 2)
{
@@ -693,7 +805,7 @@
distance1 = Math.sqrt(Math.pow(newPoint1.x - conAtomsCenter.x, 2) + Math.pow(newPoint1.y - conAtomsCenter.y, 2));
distance2 = Math.sqrt(Math.pow(newPoint2.x - conAtomsCenter.x, 2) + Math.pow(newPoint2.y - conAtomsCenter.y, 2));
}
- ringCenterVector = new Vector2d(sharedAtomsCenter);
+ ringCenterVector = new Vector2d(sharedAtomsCenter);
// no ring is attached if the two ditances are equal
if (distance1 == distance2)
{
@@ -734,10 +846,10 @@
}
makeRingAromatic(newRing);
}
-
+
// place the new atoms of the new ring to the right position
ringPlacer.placeFusedRing(newRing, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);
-
+
// removes the highlighed bond and its atoms from the ring to add only
// the new placed atoms to the AtomContainer.
try
@@ -762,7 +874,7 @@
r2dm.fireChange();
fireChange();
}
-
+
/*************************************************************************
* LASSOMODE *
*************************************************************************/
@@ -774,18 +886,28 @@
Vector lassoPoints = r2dm.getLassoPoints();
r2dm.addLassoPoint(new Point((Point)lassoPoints.elementAt(0)));
int number = lassoPoints.size();
- int[] xPoints = new int[number];
- int[] yPoints = new int[number];
+ logger.debug("# lasso points: " + number);
+ int[] screenLassoCoords = new int[number*2];
Point currentPoint;
for (int i = 0; i < number; i++) {
currentPoint = (Point)lassoPoints.elementAt(i);
- xPoints[i] = currentPoint.x;
- yPoints[i] = currentPoint.y;
+ screenLassoCoords[i*2] = currentPoint.x;
+ screenLassoCoords[i*2+1] = currentPoint.y;
+ logger.debug("ScreenLasso(.x .y) = " + screenLassoCoords[i*2] + ", " + screenLassoCoords[i*2+1]);
}
/* Convert points to world coordinates as they are
in screen coordinates in the vector */
- xPoints = getWorldCoordinates(xPoints);
- yPoints = getWorldCoordinates(yPoints);
+ int[] worldCoords = getWorldCoordinates(screenLassoCoords);
+ logger.debug("Returned coords: "+ worldCoords.length);
+ logger.debug(" # points: "+ number);
+ int[] xPoints = new int[number];
+ int[] yPoints = new int[number];
+ for (int i = 0; i < number; i++) {
+ xPoints[i] = worldCoords[i*2];
+ yPoints[i] = worldCoords[i*2+1];
+ logger.debug("WorldCoords(.x .y) = " + worldCoords[i*2] + ", " + worldCoords[i*2+1]);
+ logger.debug("Polygon(.x .y) = " + xPoints[i] + ", " + yPoints[i]);
+ }
Polygon polygon = new Polygon(xPoints, yPoints, number);
r2dm.setSelectedPart(getContainedAtoms(polygon));
r2dm.getLassoPoints().removeAllElements();
@@ -945,7 +1067,7 @@
/**
* Returns a Bond if it is in a certain range of the given point.
* Used to highlight a bond that is near the cursor.
- *
+ *
* <p><b>Important: the coordinates must be given in world
* coordinates and not in screen coordinates!
*
@@ -1101,6 +1223,7 @@
for (int i = 0; i < atomCon.getAtomCount(); i++)
{
currentAtom = atomCon.getAtomAt(i);
+ logger.debug("Atom: " + currentAtom.toString());
if (polygon.contains(new Point((int)currentAtom.getX2D(), (int)currentAtom.getY2D())))
{
selectedPart.addAtom(currentAtom);
@@ -1125,18 +1248,23 @@
/**
* This methods corrects for the zoom factor, and thus transforms
* screen coordinates back into world coordinates.
+ * IMPORTANT: even coords are taken as y coordinates, uneven as
+ * x coordinates.
*/
private int[] getWorldCoordinates(int[] coords) {
int[] worldCoords = new int[coords.length];
int coordCount = coords.length / 2;
+ logger.debug("coord.length: " + coords.length);
int height = (int)(r2dm.getBackgroundDimension()).getHeight();
for (int i=0; i<coordCount; i++) {
- worldCoords[i] = (int)((double)coords[i] / r2dm.getZoomFactor());
- worldCoords[i+1] = height - (int)((double)coords[i+1] / r2dm.getZoomFactor());
+ worldCoords[i*2] = (int)((double)coords[i*2] / r2dm.getZoomFactor());
+ logger.debug("getWorldCoord: " + coords[i*2] + " -> " + worldCoords[i*2]);
+ worldCoords[i*2+1] = (int)((double)(height - coords[i*2+1]) / r2dm.getZoomFactor());
+ logger.debug("getWorldCoord: " + coords[i*2+1] + " -> " + worldCoords[i*2+1]);
}
return worldCoords;
}
-
+
/**
* Adds a change listener to the list of listeners
*
|